
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  --------------- 06/2006            #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

# Molecule1: number of CA atoms    5 (   24),  selected    5 , name T0322TS239_4_2-D1
# Molecule2: number of CA atoms  128 (  980),  selected  128 , name T0322_D1.pdb
# PARAMETERS: T0322TS239_4_2-D1.T0322_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      G      16           -
LGA    -       -      F      17           -
LGA    -       -      S      18           -
LGA    -       -      Q      19           -
LGA    -       -      L      20           -
LGA    -       -      N      21           -
LGA    -       -      W      22           -
LGA    G      16      S      23          1.112
LGA    F      17      R      24          1.786
LGA    S      18      G      25          1.149
LGA    Q      19      F      26          3.180
LGA    -       -      G      27           -
LGA    -       -      R      28           -
LGA    -       -      Q      29           -
LGA    -       -      I      30           -
LGA    -       -      G      31           -
LGA    -       -      P      32           -
LGA    -       -      L      33           -
LGA    -       -      F      34           -
LGA    -       -      E      35           -
LGA    -       -      H      36           -
LGA    -       -      R      37           -
LGA    -       -      E      38           -
LGA    -       -      G      39           -
LGA    -       -      P      40           -
LGA    -       -      G      41           -
LGA    -       -      Q      42           -
LGA    -       -      A      43           -
LGA    -       -      R      44           -
LGA    -       -      L      45           -
LGA    -       -      A      46           -
LGA    -       -      F      47           -
LGA    -       -      R      48           -
LGA    -       -      V      49           -
LGA    -       -      E      50           -
LGA    -       -      E      51           -
LGA    -       -      H      52           -
LGA    -       -      H      53           -
LGA    -       -      T      54           -
LGA    -       -      N      55           -
LGA    -       -      G      56           -
LGA    -       -      L      57           -
LGA    -       -      G      58           -
LGA    -       -      N      59           -
LGA    -       -      C      60           -
LGA    -       -      H      61           -
LGA    -       -      G      62           -
LGA    -       -      G      63           -
LGA    -       -      M      64           -
LGA    -       -      L      65           -
LGA    -       -      M      66           -
LGA    -       -      S      67           -
LGA    -       -      F      68           -
LGA    -       -      A      69           -
LGA    -       -      D      70           -
LGA    -       -      M      71           -
LGA    -       -      A      72           -
LGA    -       -      W      73           -
LGA    -       -      G      74           -
LGA    -       -      R      75           -
LGA    -       -      I      76           -
LGA    -       -      I      77           -
LGA    -       -      S      78           -
LGA    -       -      L      79           -
LGA    -       -      Q      80           -
LGA    -       -      K      81           -
LGA    -       -      S      82           -
LGA    -       -      Y      83           -
LGA    -       -      S      84           -
LGA    -       -      W      85           -
LGA    -       -      V      86           -
LGA    -       -      T      87           -
LGA    -       -      V      88           -
LGA    -       -      R      89           -
LGA    -       -      L      90           -
LGA    -       -      M      91           -
LGA    -       -      C      92           -
LGA    -       -      D      93           -
LGA    -       -      F      94           -
LGA    -       -      L      95           -
LGA    -       -      S      96           -
LGA    -       -      G      97           -
LGA    -       -      A      98           -
LGA    -       -      K      99           -
LGA    -       -      L     100           -
LGA    -       -      G     101           -
LGA    -       -      D     102           -
LGA    -       -      W     103           -
LGA    -       -      V     104           -
LGA    -       -      E     105           -
LGA    -       -      G     106           -
LGA    S     142      E     107          2.818
LGA    -       -      G     108           -
LGA    -       -      E     109           -
LGA    -       -      L     110           -
LGA    -       -      I     111           -
LGA    -       -      S     112           -
LGA    -       -      E     113           -
LGA    -       -      E     114           -
LGA    -       -      D     115           -
LGA    -       -      M     116           -
LGA    -       -      L     117           -
LGA    -       -      F     118           -
LGA    -       -      T     119           -
LGA    -       -      V     120           -
LGA    -       -      R     121           -
LGA    -       -      G     122           -
LGA    -       -      R     123           -
LGA    -       -      I     124           -
LGA    -       -      W     125           -
LGA    -       -      A     126           -
LGA    -       -      G     127           -
LGA    -       -      E     128           -
LGA    -       -      R     129           -
LGA    -       -      T     130           -
LGA    -       -      L     131           -
LGA    -       -      I     132           -
LGA    -       -      T     133           -
LGA    -       -      G     134           -
LGA    -       -      T     135           -
LGA    -       -      G     136           -
LGA    -       -      V     137           -
LGA    -       -      F     138           -
LGA    -       -      K     139           -
LGA    -       -      A     140           -
LGA    -       -      L     141           -
LGA    -       -      S     142           -
LGA    -       -      A     143           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    5  128    5.0      5    2.18     0.00      3.219     0.219

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.046175 * X  +   0.336585 * Y  +  -0.940520 * Z  +  -5.885486
  Y_new =  -0.599060 * X  +  -0.762762 * Y  +  -0.243560 * Z  +   9.003462
  Z_new =  -0.799372 * X  +   0.552182 * Y  +   0.236855 * Z  + -24.338926 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.165590   -1.976002  [ DEG:    66.7834   -113.2166 ]
  Theta =   0.926249    2.215344  [ DEG:    53.0701    126.9299 ]
  Phi   =  -1.647723    1.493870  [ DEG:   -94.4076     85.5924 ]
 
# END of job
REMARK  ---------------------------------------------------------- 
REMARK   Citing LGA: 
REMARK   Zemla A., LGA - a Method for Finding 3D Similarities in  
REMARK   Protein Structures, Nucleic Acids Research, 2003, V. 31, 
REMARK   No. 13, pp. 3370-3374. 
REMARK  ---------------------------------------------------------- 
REMARK   Superimposed MOLECULES (1=>2)   Output: 1 molecule      
REMARK     1: T0322TS239_4_2-D1                             
REMARK     2: T0322_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0322TS239_4_2-D1.T0322_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    5  128   5.0    5   2.18    0.00   3.219
REMARK  ---------------------------------------------------------- 
MOLECULE T0322TS239_4_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0322
PARENT 1vh5_A
ATOM     76  N   GLY    16       9.230  -0.782   0.489  1.00  9.99
ATOM     77  CA  GLY    16      10.652  -0.592   0.329  1.00  9.99
ATOM     78  C   GLY    16      11.065  -0.108  -1.057  1.00  9.99
ATOM     79  O   GLY    16      12.255  -0.119  -1.378  1.00  9.99
ATOM     80  N   PHE    17      10.093   0.318  -1.867  1.00  9.99
ATOM     81  CA  PHE    17      10.398   0.888  -3.199  1.00  9.99
ATOM     82  C   PHE    17       9.565   2.137  -3.417  1.00  9.99
ATOM     83  O   PHE    17       8.881   2.596  -2.516  1.00  9.99
ATOM     84  CB  PHE    17      10.298  -0.165  -4.330  1.00  9.99
ATOM     85  N   SER    18       9.595   2.682  -4.631  1.00  9.99
ATOM     86  CA  SER    18       9.011   4.001  -4.843  1.00  9.99
ATOM     87  C   SER    18       7.503   4.028  -4.559  1.00  9.99
ATOM     88  O   SER    18       6.987   5.018  -4.048  1.00  9.99
ATOM     89  CB  SER    18       9.292   4.495  -6.267  1.00  9.99
ATOM     90  N   GLN    19       6.804   2.966  -4.939  1.00  9.99
ATOM     91  CA  GLN    19       5.363   2.920  -4.731  1.00  9.99
ATOM     92  C   GLN    19       5.060   3.094  -3.215  1.00  9.99
ATOM     93  O   GLN    19       4.203   3.887  -2.839  1.00  9.99
ATOM     94  CB  GLN    19       4.729   1.624  -5.304  1.00  9.99
ATOM    639  N   SER   142       9.105 -13.125 -22.693  1.00  9.99
ATOM    640  CA  SER   142       8.711 -14.518 -22.634  1.00  9.99
ATOM    641  C   SER   142       9.593 -15.234 -21.644  1.00  9.99
ATOM    642  O   SER   142       9.154 -16.173 -20.993  1.00  9.99
ATOM    643  CB  SER   142       8.778 -15.164 -24.049  1.00  9.99
TER
END
